Phylogenetic models of rate heterogeneity: a high performance computing perspective

By Alexandros Stamatakis. Proceedings 20th IEEE International Parallel & Distributed Processing Symposium, 2006

415 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Paleontology

View Paper: https://www.semanticscholar.org/paper/5bd7059df74179ec8eaede5513a7e1cf80fff5e3

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Citations in the corpus

Molecular phylogeny of the Calyptratae (Diptera: Cyclorrhapha) with an emphasis on the superfamily Oestroidea and the position of Mystacinobiidae and McAlpine's fly (2010, methodology): “, 2005) to bootstrap the dataset (250 replicates) on the CIPRES computer cluster (Cyberinfrastructure for Phylogenetic Research; San Diego Supercomputing Center) using the GTR + CAT model (Stamatakis, 2006).”
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments (2010, methodology): “Thus, it is much faster, and just as accurate, to use a good estimate of the rate at each site (CAT) rather than to sum over four potential rates (C4) [14].”
Applied aspects of methods to infer phylogenetic relationships amongst fungi (2020, methodology): “…various models of evolution with different non-parametric bootstrapping iterations. e.g. RAxML (Randomized acc(x)elerated maximum likelihood) RAxML is the fastest available software to run heuristic ML analysis on large datasets, which may include thousands of sequences (Stamatakis 2006).”
A rapid bootstrap algorithm for the RAxML Web servers. (2008, methodology): “(Stamatakis, 2006a, 2006b).”
Building the Coleoptera tree‐of‐life for >8000 species: composition of public DNA data and fit with Linnaean classification (2014, methodology): “Tree searches were performed under maximum likelihood (ML) in RAxML (Stamatakis, 2006) on the CIPRES web server (Miller et al., 2010), using the GTRCAT model partitioned by gene and by codon position for cox1 .”
Identifying the sister group to the bees: a molecular phylogeny of Aculeata with an emphasis on the superfamily Apoidea (2012, methodology): “3000 rapid bootstrap replicates were performed using GTR+CAT, which approximates a GTR+I+G model (Stamatakis 2006b).”
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models (2006, methodology): “Finally, the experimental study also shows that the GTR+CAT approximation [see Stamatakis (2006) for a detailed description] can be efficiently deployed as a replacement for the significantly more computeand memory intensive GTR+G model.”
Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood (2011, positive): “In order to more rapidly compute the per-edge insertions of the QS, we use an approximation that is comparable with the lazy subtree rearrangement (LSR) moves that are deployed in the standard RAxML search algorithm (see Stamatakis et al. 2005).”
A new genus and species of rodent from the Brazilian Atlantic Forest (Rodentia: Cricetidae: Sigmodontinae: Oryzomyini), with comments on oryzomyine biogeography (2011, methodology): “Nodal bootstrap values (Felsenstein, 1985) for the likelihood analysis were calculated using 1000 pseudoreplicates under the GTRCAT model in RAxML (Stamatakis, 2006b).”
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. (2010, methodology): “2009), both running the CAT approximation of the gamma rate distribution with four bins (Stamatakis 2006b).”